Gene doping is banned in human sports,
horseracing, and equestrian
sports. One possible form of gene doping is to administer exogenous
genes, called transgenes. Several transgene detection methods based
on quantitative PCR have been developed. In this study, we investigated
the robustness of digital PCR and real-time PCR in transgene detection
using primers and probes that matched (P-true) or incompletely matched
(P-false) the template DNA. Fluorescence intensity was significantly
reduced when substituted probes were used compared to that using the
matched probe in both digital and real-time PCR assays. Digital PCR
yielded a similar copy number regardless of the probe (P-true: 1230.7,
P-false: 1229.7), whereas real-time PCR revealed a decrease in sensitivity
based on C
q values (P-true: 23.5, P-false:
29.7). When substituted primers were used, the detected copy number
decreased in the digital PCR assay, and the C
q value in real-time PCR was much higher. Interestingly, digital
PCR copy numbers improved by performing PCR at a low annealing temperature,
even if a substituted probe was used. Thus, when primer and probe
sequences did not completely match the template transgene, digital
PCR was relatively robust, but real-time PCR was less sensitive. Although
PCR specificity may be reduced, PCR sensitivity can be improved by
lowering the annealing temperature. If the target sequence is substituted
to escape doping detection, it may be desirable to set the annealing
temperature lower and use a more robust method, such as digital PCR,
to increase the detection of positive cases, which will also result
in fewer false-negative results.